28 February 2014

I spent a good chunk of today in a symposium about dual career hiring in academia. While the problem tuns throughout all of higher education, the focus was on STEM. I live tweeted as many talks as I could attend before I had to run off to class.

Our president said he was going to support dual hires, though the shape of this isn’t clear yet. But when you have buy-in from administration at the top, it makes things a lot easier. I hope that when be become a new university, we will be able to build in dual hire policies from the ground floor.

In conversation over lunch, I asked one speaker about whether state laws would prevent dual hires. She said no, because most nepotism laws had been struck down for being discriminatory against women. This interested me, given how often our search committee had been instructed to consider someone’s ability to do the job, and only their work related abilities, for legal reasons. There is clearly much more room to maneuver on these matters than I thought, and I’ve been done a lot of search committees.

I thank Biochembelle profusely, who took it upon herself to Storify my tweets:

19 February 2014

This is repetitive. Another week, another academic publisher, another “me too” Zune journal. The latest to imitate PLOS ONE is the Royal Society, which announced it is launching Royal Society Open Science.

Let’s count the similarities to PLOS ONE, shall we?

Supported by article fees. To their credit, however, there will be no fees for the first year. Honestly, I might submit an article while it’s free, but probably not after that. Why pay a fee more than ten times the cost of PeerJ?

Does not review for “impact.”

Article level metrics.

Innovations? Maybe that there is an option for open peer review. But it’s not clear what that will look like, so it’s hard to tell.

Like Science Advances, Royal Society Open Science will also “accept articles referred from other Royal Society journals.” Nice, but you do not need a new journal specifically to do that. As I noted before, it’s not clear what advantage having an article “referred” to this journal has versus taking my article to another non-Royal Society journal. Plus, why not accept articles referred from a lot of other journals besides Royal Society journals?

I just don’t see the point of this journal. I just don’t get what this journal is supposed to do for me that a ream of existing journals don’t already for me.

Unless you read very carefully, this news article from Science makes it seem like this is the Society’s first foray into open access publishing, but it is not. They already have Open Biology, running since 2011. It is still free to publish in Open Biology, even after more than two full years of publication. This might suggest that this “selective” new journal is not attracting the number of articles that it would like to.

I also note that, unlike Science, Royal Society journals have had the option of authors paying a (hefty) fee to make article open access for a while now.

I’m also puzzled by Steve Harnad’s pokes against the “gold” model of open access. We are just nowhere near enough institutions creating repositories for authors to self-archive to do the job. Maybe it will evolve towards that, but I don’t think that model is ready yet.

Perhaps the take home message from these new open access journals is this:

The creation of PLOS ONE was a landmark in the history of early twenty-first scientific publishing. Look at how many publishers have taken the PLOS ONE model, and run with it, and added no real innovations. Love it or hate it, you cannot ignore PLOS ONE. It changed the landscape of scientific publishing – and I would say for the better – more than anything else I can think of since the millenium.

17 February 2014

I am heartened that Science’s publisher, American Association for the Advancement of Science (AAAS) actually is listening to critics. This article notes that AAAS “has long been a target of complaints from some advocates of open-access publishing.” I wrote that Science magazine was a prime target to become an open access journal a little over two years ago. I don’t pretend my little blog post had much impact, but maybe Michael Eisen posting of a bunch of Mars Curiosity rover papers that had been paywalled by Science did have an effect. It made news.

Unfortunately, that has not happened. Instead of doing what open access advocates have, well, advocated – making Science the world’s first glamour mag to go open access – AAAS is creating Science Advances. This is, as far as I can see, another Zune journal: a “me too” journal with no apparent innovations.

Responding to criticism by creating something that nobody asked for is maybe not the strongest public relation move.

Let’s look at the rationale for creating yet another journal rather than improving the ones we have.

Science and AAAS’s other journals have been forced to turn away many high-quality papers, without providing an alternative publication venue.

But there already are alternative publication venues. There are many other journals by other publishers, including scientific societies. What advantage is there to authors in having this new journal? Maybe this:

Papers submitted to Science or its sister journals, Science Translational Medicine and Science Signaling, that are rejected can be automatically considered for Science Advances without more reviews.

You don’t need a new journal to do this; you just need cooperation between existing journals. Some neuroscience journals do this: check the Neuroscience Peer Review Consortium.

If there are positive reviews from Science, will acceptance be (almost) automatic in Science Advances? If the editorial board and review process is independent of Science, it may not be automatic, and authors may have to have to face another round of reviews, probably by different people. If that’s the case, there is no obvious advantage to authors to have this AAAS journal compared to another open access journal.

Another question is whether Science Advances will be review papers for intangibles like “impact,” “novelty,” and “importance.” If Science Advances simply goes for technical soundness, like PLOS ONE, many authors may want to pull their paper from the Science Advances submission queue to try their hand at an established disciplinary journal. An existing disciplinary journal will probably have a stronger brand than an untried Zune journal, regardless of the publisher.

Science Advances is a distraction from the real issues. I wish publishers would stop trying to give us what we don’t want. I would rather they just address the question of why it’s so difficult for their journals, like Science, to have their original technical articles to be open access.

Additional, 19 February 2014: Naturereports that Science Advances will screen articles for “import,” not just technical soundness. That seems to me that it is competing in a very most crowded niche in scientific publishing. There are a lot of journals that know that won’t reach into the realm of Science, Nature, and Cell, but strive to be the first line for papers that don’t make it there.

13 February 2014

One year ago, I predicted the new journal DeNovo would never have a second issue.

You may recall that the journal published a single article in its first issue, one by Melba Ketchum, claiming to have found evidence for new hominins in North America. That it, sasquatch DNA. Many people charged that the creation of DeNovo was a pure “vanity press” move by Ketchum to publish her research. Ketchum denied this. But there is little doubt she have a very, very steep uphill climb to get the paper in any regular scientific journal.

I cannot say that DeNovo is a dead website. The look of the
website has changed since I last checked it, so someone is minding the
store. The appearance is still fairly dreadful, though, with lots of
crummy, pixelated images in the banner.

As for the scientific content, not only has there never been a second issue, there has never been a second article. It’s things like this that give new journals, and new publication models, like open access publishing, a bad name.

I happen to employ polarized light often in my photography. And not to cut reflections, but to find interesting patterns in different animals. In fact, most of my images in the old microscope gallery are made using polarized light microscopy technique that happens to emphasize muscles and other regular structures. After reading a lot about vision systems in invertebrates ...

The authors studied polarization vision in one amphipod species and gave evidence that it uses it for navigation. This work made me remember that some amphipods look very spectacular in polarized light, mostly from photos posted in photomicrography.net community. I decided to catch a few random amphipods (not of the same species) and make focus stacks under high magnification with crossed polarizers. I was amazed, to say the least! These guys are fabulous and all these patterns are absolutely invisible to our eyes.

06 February 2014

For those not familiar with the kelvin scale, 100 kelvin is -173°C. But soon after I saw this, I read a paper that is going to require a slight modification to this graph:

Meet the animal that forced the rewrite: Ozobranchus jantseanus.

This is a leech that lives on Japanese turtles. Some turtles can spend most of the winter under ice, so they get very cold, which in turn means anything on them will also get very cold. Cold is a problem for animals, for reasons you can see in this video:

The can is actually a good model for why freezing is bad for organisms. Water is weird: it expands when it freezes. If you think of the can as being like a cell, freezing causes all sorts of damage. Some species are able to tolerate freezing temperatures with biological antifreezes and other tricks.

But very fee are able to take it to the extreme of the leech above.

Suzuki and colleagues (2014) tested seven different species leeches, and froze then at -90°C.

Six of those species died. Ozobranchus jantseanus lived. Not only that, they could survive being frozen at -90°C for almost a year. And they could be frozen and thow out again up to five times before suffering any mortality.

Not content, Suzuki and colleagues decided to up the ante. They dropped these animals into liquid nitrogen, and left them there for 24 hours. All of them (tried with five individuals) revived when they were thawed back up, and lived over a month. Now, the animals that were frozen were not entirely normal. They couldn’t stretch the way they could before hand, but they were most definitely alive, moving under their own power.

This stunned me, and I thought for sure that this must be a record holder. But it turns out that there are a few other species that can take extreme temperatures, with the coldest being the larva of a fly (Polypedilum vanderplanki) that can survive a stunning -270°C. It does this by drying itself out completely, virtually becoming a living rock (“vitrifcation”).

How the leeches are doing this is not worked out at all in this paper. It must be some standing feature of the animal, because they are essentially flash frozen. There is not time for any sort of physiological or cellular response to kick in from a reaction to the cooling.

This is a very cool result (pun intended). One of the research groups that must be excited about this are the people interested in exobiology and the prospects of life on other planets. If something can survive these sorts of extremes, it significantly stretches the possible environments in which we might find life.

And this post gives me an excuse to feature one of my favourite movie musical numbers in years, this show stopper from Frozen:

05 February 2014

People love templates. They can be great time-savers. But in the context of presentations, people often think of templates for PowerPoint slides, which are often overly busy and not well designed. Instead of using templates for slide design, try using a template for the script of your talk.

In Connection: Hollywood Storytelling Meets Critical Thinking (reviewed here), Dorie Barton is quoted as saying, “Dude, it’ all the same story.” At SICB last month, Barton’s co-author, Randy Olson, elaborated. He talked about how a scientific paper can, in very broad strokes, follow Joseph Campbell’s “hero’s journey.” A key component of the monomyth is that there is an “ordinary world” (on top in the figure below) and a “special world” (on the bottom of the figure below).

The ordinary world is what is routine and familiar (think Kansas, Tatooine, the Shire); the special world is unknown, exciting, but also exhausting and dangerous (think Oz, the Death Star, Mordor). Olson pointed out that a scientific paper always starts off with the boring, mundane, and the known (Introduction). It may be the reason the first sentences of scientific papers are notoriously bland and general.

The paper then ventures into the unknown (Methods and Results), the new territory that the researchers are hoping to uncover. They then take what they learn, and bring it back to the ordinary world that they started in (Discussion).

Another strong structure for presentations is the “worm” presentation structure discussed by Nancy Duarte in her book Resonate (it’s now available in a free online version here; reviewed here).

The core of a presentation structure, according to Duarte, is the contrast between “what is” and “what could be.” Again, scientific research often has the core of Duarte’s “worm” presentation structure built into it .

The “what is” is our background knowledge. The “what could be” is typically our hypotheses and predictions (click to enlarge).

As I said recently:

(T)here is an inherent connection between stories and experimental science: they are both about causes. A satisfying story is built around causal connections.

Good presentations can be analyzed in many different ways. For instance, the Gettysburg address follows both Randy Olson’s “And, but, therefore” template (analysis here), and Nancy Duarte’s “what is / what could be” presentation structure (analysis here).